International University Biotechnology Biochemistry

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Definition and basic process: 1. Induced fit 2. Mechanisms of transition state stabilization • Detailed in example to make you understand more about mechanism of enzyme catalyst: Chymotripsin

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Nội dung Text: International University Biotechnology Biochemistry

International University Biotechnology Biochemistry Lecturer: Msc. Le Hong Phu
Topic 9: Detailed Mechanism of Enzyme Catalyst • Group Members: 1. Do Ngoc Anh Huy 2. Tran Van Kha 3. Doan Luong Huy 4. Dang Duong Group leader 5. Nguyen Quang Toan 6. Nguyen Thi Huong Giang 7. Pham Vinh Phuoc
Content: • Definition and basic process: 1. Induced fit 2. Mechanisms of transition state stabilization • Detailed in example to make you understand more about mechanism of enzyme catalyst: Chymotripsin
Lock-key theory • A Specific active site for a specific substrate How can make the key to be fixed to the locker???
Induced fit theory • The initial reaction between E and S is weak, but it rapidly induce by conformational changes in the enzyme.
The transition state • When a chemical reaction occurs, the energy content of the reacting molecule or atom increases. • This is why most chemical reactions, whether they release heat or absorb heat. • The high-energy state of the reactants is called the transition state.
Mechanisms of transition state stabilization • These conformational changes also bring catalytic residues in the active site close to the chemical bonds in the substrate that will be altered in the reaction. • One or more mechanisms of catalysis lowers the energy of the reaction's transition state, by providing an alternative chemical pathway for the reaction.
6 possible cases of mechanism 1. Catalysis by bond strain 2. Catalysis by proximity and orientation 3. Acid/Base catalysis 4. Electrostatic catalysis 5. Covalent catalysis 6. Quantum tunneling
Catalysis by bond strain • This is the principal transition effect of induced fit Bound state Substrate conformatio subtrate binding, where the ns affinity of the enzyme to the transition state is greater than to the substrate itself. • Bond strain induces structural rearrangements • At lowering the energy difference between the substrate and transition state and helping catalyze the reaction.
Catalysis by Approximation  Definition: • This increases the rate of the reaction as enzyme-substrate interactions align reactive chemical groups and hold them close together. • This reduces the entropy of the reactants (ligations or addition) reactions more favorable, proximity Catalysis by Approximation orientation
An enzyme increases the rate of a bimolecular Proximity reaction is to use binding energy to simply bring the two reactants in close proximity ATP P P P rib Glucose P Glucose
Orientation – Even when two molecules collide with enough energy to cause a reaction, they don't necessarily form products. – They have to be oriented – Enzymes bind substrates the reactive groups are steered to the direction that can lead to a reaction
Catalytic involving proton donors and acceptor (acid/base catalysis) • Proton donors and protease Serine acceptors, like acids mechanism catalytic and bases, may donate and accept protons in order to stabilize developing charges in the transition state. This typically has the effect of activating nucleophile and electrophile groups, or stabilizing leaving groups. Histidine is often the residue involved in these acid/base reactions, since it has a pKa close to neutral pH and can therefore both accept and donate protons
Proton donors and acceptors, i.e. acids and bases, may donate and accept protons in order to stabilize developing charges in the transition state Conditions Acids Base Hydrophobic Increase pKa Decrease pKa Adjacent Increase pKa Decrease pKa residues of like charge Decrease pKa Increase pKa Salt bridge (and hydrogen bond) formation
ionic Electrostatic catalysis • Stabilization of charged transition states can also be by residues in the active site forming bonds (or partial ionic charge interactions) with the intermediate. • These bonds are formed from acidic or basic side chains(lysine, arginine, aspartic acid or glutamic acid),or form metal cofactors(zinc) • Electrostatic effects are the largest contribution to catalysis
Ex:
Covalent catalysis Involves the substrate forming a transient covalent bond with residues at the active site or with a cofactor.
Quantum tunneling • Some enzymes operate with kinetic which is faster than diffusion rate , which would seem to be impossible Go to explain by quantum tunneling!!! • Quantum mechanics allows a small particle, such as an electron or proton, to overcome a potential barrier larger than its kinetic energy
Chymotrypsin • Chymotrypsin is synthesized in the pancreas by protein synthesis as a precursor called chymotrypsinogen that is enzymatically inactive. • Amino-link system include: Histidine 57, Serine 195, Asparagine 102.